-
I am performing differential gene expression analysis using the CIRIquant pipeline. Referring to the CIRIquant cookbook, I successfully arrived into this step:
"Usage 3: Differential expression ana…
-
Hi
I ran the CIRIquant and everythings goes well but it generate empty gtf file (only has header as follow
##Sample: test
##Total_Reads: 8767472
##Mapped_Reads: 8257908
##Circular_Reads: 0
##ver…
-
On 12/02/20 Takanobu wrote:
>Another possibility would be to look at ratio between linear RNA reads vs circular RNA reads, and pick circRNAs that has the ratio above certain threshold. I recently (re…
-
Dear CIRIquant developers,
After over 1 hour running CIRIquant, I'm getting stuck with following error(s):
#########################################################
[Tue 2021-03-09 03:24:07] [INF…
-
I attach below the full CLEAR pipeline with STAR alignment in case someone needs:
```
# define parameters
file_extension="_1.fq.gz"
read_length=100
ref_genome="hg19"
# download reference fil…
-
Taka reported:
`
I still have a bit of problem understanding count_matrix_with_annotations.txt. Is this combining all BSJs (back-splice junctions) detected, or only “known” BSJs are included? if you…
-
Dear YangLab
You guys have done an amazing piece of work. Thanks for that.
I have a question I tried to do circRNAs detection using this pipeline but in the annotation module we require a ref file…
-
cd ~/biosoft
cd NCLscan
./NCLscan.py -c ./NCLscan.config -pj clean -o output --fq1 EGAR00001653004_1.fastq.gz --fq2 EGAR00001653004_2.fastq.gz
Unknown command "view".
[M::bwa_idx_load_from_di…
-
Hi, Dr JAKOBI,
I download the FUCHS from github and using the install code you provided, however, when I use the command
" python setup.py install --user"
The process failed for there is lack of…
-
Hi,
I've been working on a set of samples using the differential expression analysis for biological replicates. All steps work fine until I get to using CIRI_DE_replicate, where I get the followin…